Publications
Journal articles, manuscripts, book chapter, and selected proceedings.
Published Papers in International Journals
- 2027 — ALTINTAN DERYA, AYDIN E., YILMAZ F., TEMOCIN B. Z. “A new numerical scheme for stochastic control problems of jump-diffusion equations by means of Runge–Kutta method.” Journal of Computational and Applied Mathematics, 489, 15.
- 2026 — ALTINTAN DERYA. “Modified delay chemical master equation and two simulation methods to approximate its solution.” Communications in Statistics–Simulation and Computation, 25.
- 2026 — ALTINTAN DERYA. “Hybrid stochastic algorithms for simulating delayed biochemical reaction networks with monomolecular subsystems.” International Journal of Computer Mathematics, 21.
- 2026 — YILMAZ F., AYDIN E., TEMOCIN B. Z., ALTINTAN DERYA. “Strong Order Runge–Kutta Method for Stochastic Optimal Control Problems of the Merton Jump Diffusion Model.” Optimal Control Applications & Methods, 47(2), 13.
- 2025 — GÜLNÍHAL MERAL, ALTINTAN DERYA. “Mathematical modeling and analysis for Michaelis–Menten kinetics.” Journal of Mathematical Chemistry, 1–14.
- 2020 — ALTINTAN DERYA, KOEPPL HEINZ. “Hybrid Master Equation for Jump-Diffusion Approximation of Biomolecular Reaction Networks.” BIT Numerical Mathematics, 60, 261–294.
- 2018 — ALTINTAN DERYA, PURUTÇUOĞLU GAZİ VİLDA. “Exact Stochastic Simulation Algorithms and Impulses in Biological Systems.” International Journal of Computational and Experimental Science and Engineering (IJCESEN), 4(2), 41–47.
- 2018 — ALTINTAN DERYA, PURUTÇUOĞLU GAZİ VİLDA, UĞUR ÖMÜR. “Impulsive Expressions in Stochastic Simulation Algorithms.” International Journal of Computational Methods, 15, 170075.
- 2015 — GANGULY ARNAB, ALTINTAN DERYA, KOEPPL HEINZ. “Jump diffusion approximation of stochastic reaction dynamics: Error Bounds and Simulation.” SIAM Journal of Multiscale Modelling and Simulation, 13(4), 1390–1419.
- 2013 — ALTINTAN DERYA, UĞUR ÖMÜR. “Solution of Initial and Boundary Value Problems by the Variational Iteration Method.” Journal of Computational and Applied Mathematics, 259, 790–797.
- 2011 — ALTINTAN DERYA, UĞUR ÖMÜR. “Generalisation of the Lagrange multipliers for variational iterations applied to systems of differential equations.” Mathematical and Computer Modelling, 54, 2040–2050.
- 2010 — JAHNKE TOBIAS, ALTINTAN DERYA. “Efficient simulation of discrete stochastic reaction systems with a splitting method.” BIT Numerical Mathematics, 50(4), 797–822.
- 2009 — ALTINTAN DERYA, UĞUR ÖMÜR. “Variational iteration method for Sturm-Liouville differential equations.” Computers & Mathematics with Applications, 58(2), 322–328.
Submitted, Under Review, and Preprints
- ALTINTAN DERYA. [Under Review] “Time-Dependent Information Security Risk Assessment via Epidemic Modeling and Neural Surrogates.” Applied Mathematics and Computation, 2026.
- ALTINTAN DERYA; GÜLNÍHAL MERAL. [Under Review] “Existence, Positivity and Conservation-Based Reduction in Dual Phosphorylation Modules of MAPK Pathways.” Journal of Mathematical Chemistry, 2026.
- ALTINTAN DERYA, ALT BASTIAN, KOEPPL HEINZ. [Preprint] “Bayesian inference for jump-diffusion approximations of biochemical reaction networks.” arXiv preprint, arXiv:2304.06592, 2023.
Chapter in Book
- ALTINTAN DERYA, DIEMER JASHA, KOEPPL HEINZ. “Analysis and Modeling of Single Cell Data.” In Systems of Immunology, Taylor & Francis.
Papers Published in National Journals
- 2021 — BÜŞRANUR OĞRAŞ, DERYA ALTINTAN. “Biyokimyasal Reaksiyon Sistemlerinin Modellenmesi için Deterministik ve Stokastik Yaklaşım.” Selcuk University Journal of Science Faculty, 47(1), 1–15.
- 2016 — ALTINTAN DERYA. “Korunumlu döngülerin stokastik simülasyon algoritmalarında kullanımı.” Sakarya Universitesi Fen Bilimleri Enstitüsü Dergisi, 20(3), 617–625.
Proceedings
- 2025 — ALTINTAN DERYA. “Modeling Malware Spread in Information Security Systems using a Stochastic SEIR-Neural Network Approach.” International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2025).
- 2016 — YAZICI MÜGE, PURUTÇUOĞLU GAZİ VİLDA, ALTINTAN DERYA. “Application of Stochastic Simulations of Biological Networks Under Different Impulsive Scenarios.” Proceedings of The Third International Conference on Data Mining, Internet Computing.
- 2016 — ALTINTAN DERYA, GANGULY ARNAB, KOEPPL HEINZ. “Efficient simulation of multiscale reaction networks: A multilevel partitioning approach.” ACC 2016.
- 2015 — GANGULY ARNAB, ALTINTAN DERYA, KOEPPL HEINZ. “Error bound and simulation algorithm for piecewise deterministic approximations of stochastic reaction systems.” 2015 American Control Conference.
- 2011 — AKHMET MARAT, ALTINTAN DERYA, ERGENÇ TANIL. “Chaos of the Logistic Equation with Piecewise Constant Argument.” Proceedings of Dynamic Systems and Applications.
Projects
Selected funded research projects from my academic CV.
2024–2027 · Researcher
TÜBİTAK 1001 — 124F035
Development of efficient and easy computational algorithms based on the Runge–Kutta method for stochastic optimal control problems representing financial models integrated with time delay and stochastic factors.
2024–2025 · Manager
TÜBİTAK 1002 — 124F043
Modeling of delayed biochemical reaction networks with monomolecular reaction channels.
2022 · Manager
DAAD Research Stays for Academics and Scientists
Particle Monte Carlo Markov Chain Method with Hamiltonian Monte Carlo.
2020–2022 · Researcher
METU GAP-109-2020-10282
Approximate stochastic simulation algorithms in protein interaction networks.
2015–2018 · Manager
TÜBİTAK 3501 Career Development Project
Inference and marginalization algorithms for stochastic biochemical networks with multi-scale nature and their applications.
Presentations
Conference presentations listed in my academic CV.
International Conferences
- 2026 — ALTINTAN DERYA. “A Neural-Network-Based Framework for Cryptographic Systems under Hawkes-Driven Attacks.” The 4th International Conference on Applied Mathematics in Engineering (ICAME’26), 2–4 September 2026, Balıkesir, Turkey.
- 2025 — ALTINTAN DERYA. “Modeling Malware Spread in Information Security Systems using a Stochastic SEIR-Neural Network Approach.” The 23rd International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2025), 16–22 September 2025, Heraklion, Crete, Greece.
- 2024 — ALTINTAN DERYA. “A hybrid method for simulating biochemical reaction networks with time-delay involving monomolecular reactions.” The 3rd International Conference on Applied Mathematics in Engineering (ICAME’24), 26–28 June 2024, Ayvalık–Balıkesir, Türkiye.
- 2023 — ALTINTAN DERYA, ALT B., KOEPPL H. “Blocked Gibbs Particle Smoothing Algorithm for Jump-Diffusion Approximations of Biochemical Reaction Networks.” ENUMATH 2023, 4–8 September 2023, Lisbon, Portugal.
- 2021 — ALTINTAN DERYA. “Numerical Solution Method for Delay Chemical Master Equation.” International Conference on Applied Mathematics in Engineering (ICAME), 1–3 September 2021, Balıkesir, Turkey.
- 2021 — ALTINTAN DERYA, KOEPPL HEINZ. “Inference and Marginalization Algorithms for Jump Diffusion Approximation.” International Conference on Applied Mathematics in Engineering (ICAME), 1–3 September 2021, Balıkesir, Turkey.
- 2019 — ALTINTAN DERYA, KOEPPL HEINZ. “Moment Approximation for the Joint Probability Density Function of the Jump-Diffusion Approximation.” ENUMATH 2019, 29 September–4 October 2019, Egmond aan Zee, Holland.
- 2018 — ALTINTAN DERYA, KOEPPL HEINZ. “Moment Methods for Hybrid Master Equation of Biomolecular Reaction Networks.” ICM 2018, 1–9 August 2018, Rio de Janeiro, Brazil.
- 2018 — ALTINTAN DERYA, KOEPPL HEINZ. “On Modeling Approaches of Biochemical Reaction Networks.” International Conference on Mathematics and Related Sciences (ICMRS 2018), 30 April–4 May 2018, Antalya, Türkiye.
- 2017 — ALTINTAN DERYA, GANGULY ARNAB, KOEPPL HEINZ. “Maximum Entropy Methods for Jump-Diffusion Approximations of Chemical Kinetics.” ENUMATH 2017, 25–29 September 2017, Voss, Norway.
- 2016 — PURUTÇUOĞLU GAZİ VİLDA, ALTINTAN DERYA. “Exact Stochastic Simulation Algorithms Under Different Scenarios of Biological Systems.” 2nd International Researchers-Statisticians and Young Statisticians Congress, 6–8 September 2016, Ankara, Türkiye.
- 2016 — ALTINTAN DERYA. “Stochastic Modelling with Conservation Relations.” 2nd International Researchers-Statisticians and Young Statisticians Congress, 6–8 September 2016, Ankara, Türkiye.
- 2015 — PURUTÇUOĞLU GAZİ VİLDA, ALTINTAN DERYA. “Comparison of Performances for Stochastic Simulation Algorithms of Biochemical Networks with/without Impulses.” 2nd International Conference on Computational and Experimental Science and Engineering, 14–19 October 2015, Antalya, Türkiye.
- 2015 — ALTINTAN DERYA, GANGULY ARNAB, KOEPPL HEINZ. “Hybrid Models for Multi-Scale Processes: Error Bounds and Simulation Algorithms.” ENUMATH 2015, 14–18 September 2015, Ankara, Türkiye.
- 2015 — ALTINTAN DERYA, PURUTÇUOĞLU GAZİ VİLDA, UĞUR ÖMÜR. “Functional Impulses in Exact Stochastic Simulation.” ICAPM 2015, 25–28 August 2015, Van, Türkiye.
- 2015 — GANGULY ARNAB, ALTINTAN DERYA, KOEPPL HEINZ. “Error bound and simulation algorithm for piecewise deterministic approximations of stochastic reaction systems.” 2015 American Control Conference, 3–5 July 2015, Chicago, USA.
- 2013 — ALTINTAN DERYA, PURUTÇUOĞLU GAZİ VİLDA, UĞUR ÖMÜR. “Impulsive Expression in Chemical Master Equation and Stochastic Simulation Algorithms.” 26th European Conference on Operational Research (EURO / INFORMS), 1–4 July 2013, Rome, Italy.
- 2012 — ALTINTAN DERYA, UĞUR ÖMÜR. “Solutions of Initial and Boundary Value Problems by using Variational Iteration Method.” International Conference on Applied and Computational Mathematics (ICACM), 3–6 October 2012, Ankara, Türkiye.
- 2012 — ALTINTAN DERYA, UĞUR ÖMÜR. “Logistic Equation with Stochastic Modelling Approach.” International Conference on Applied and Computational Mathematics (ICACM), 3–6 October 2012, Ankara, Türkiye.
- 2011 — ALTINTAN DERYA, UĞUR ÖMÜR. “How to solve boundary value problems by using Variational Iteration Method.” 24th Biennial Conference on Numerical Analysis, 28 June–11 July 2011, Glasgow, United Kingdom.
- 2009 — ALTINTAN DERYA, UĞUR ÖMÜR. “Generalized Multistage Variational Iteration Method.” 8th ENUMATH 2009, 29 June–3 July 2009, Uppsala, Sweden.
National Conferences
- 2023 — ALTINTAN DERYA. “Modeling and Inference Approaches for Biochemical Reaction Networks.” Computational Science, Mathematical Modeling and Engineering Conference (BEYOND 2023), 19–20 October 2023, Ankara, Turkey.
- 2015 — ALTINTAN DERYA, GANGULY ARNAB, KOEPPL HEINZ. “Çok ölçekli reaksiyon sistemleri için hibrid modelleri ve algoritmalar.” 10. Ankara Matematik Günleri, 11–12 June 2015, Ankara.
- 2014 — GANGULY ARNAB, ALTINTAN DERYA, KOEPPL HEINZ. “Stokastik reaksiyon sistemlerinin sıçramalı-difüzyon yaklaşımı: hata analizi ve algoritma.” 26. Ulusal Matematik Sempozyumu, 26–29 August 2014, İstanbul.
- 2011 — JAHNKE TOBIAS, ALTINTAN DERYA. “Stokastik Reaksiyon Sistemlerinin Ayrıştırma Metodu ile Simülasyonu.” 24. Ulusal Matematik Sempozyumu, 7–10 September 2011, Bursa.
- 2010 — AKHMET MARAT, ALTINTAN DERYA, ERGENÇ TANIL. “Parçalı sabit fonksiyonlar içeren Lojistik denklemlerin kaotik yapısı.” 23. Ulusal Matematik Sempozyumu, 4–7 August 2010, Kayseri.
Grants & Awards
Grants and scholarships listed in my academic CV.
Grants & Scholarships
- March–May 2022 — DAAD Research Grant.
- June–November 2014 — DAAD Young Academics Scholarship & TUD.
- 2013–2014 — TÜBİTAK Postdoc Fellowship.
- 2006–2011 — TÜBİTAK National Scholarship for Ph.D. Students.
- 2000–2003 — TÜBİTAK National Scholarship for B.Sc. Students.
The CV lists these items under “Grants and Scholarships”; no separate awards are listed in the supplied CV.
International Experience
International academic appointment and research experience.
International Academic Appointment
Azerbaijan · 2024–Present
Türkiye–Azerbaijan University · Baku
Associate Professor (Visiting)
Department of Mathematics · Hacettepe University Joint Program
Baku, Azerbaijan
Ongoing teaching and academic duties carried out as part of Hacettepe University’s joint program at Türkiye–Azerbaijan University.
Research Appointments & Visits
Switzerland · 2013–2014
ETH Zürich
International Postdoctoral Visiting Researcher
Automatic Control Laboratory · BISON Group
Zürich, Switzerland
Host: Prof. Dr. Heinz Koeppl
Germany · 2009–2010
Karlsruhe Institute of Technology (KIT)
Visiting Researcher
Department of Mathematics
Karlsruhe, Germany
Host: Prof. Dr. Tobias Jahnke
Technische Universität Darmstadt · Bioinspired Communication Systems
Research visits hosted by Prof. Dr. Heinz Koeppl · Darmstadt, Germany
- March–June 2023 — Research visit.
- August–September 2018 — Research visit.
- June 2018 — Research visit.
- January–February 2018 — Research visit.
- August–September 2017 — Research visit.
- January–February 2017 — Research visit.
- February 2016 — Research visit.
- September 2015 — Research visit.
- January–February 2015 — Research visit.
Teaching
Current courses and downloadable course materials. Lecture notes are organized inside each course rather than as a separate top-level menu.
MAT123 · Hacettepe University
Mathematics I
General information, lecture notes, exercise sheets, exams, assignments and announcements.
Course Page →
MAT124 · Hacettepe University
Mathematics II
General information, lecture notes, exercise sheets, exams, assignments and announcements.
Course Page →
Türkiye–Azerbaijan University
Differential Equations
Course objectives and outcomes, lecture notes, Laplace transform table, exams, assignments and announcements.
Course Page →
Course passwords will be configured at the hosting level. They are not embedded in this HTML file.
← Back to Teaching2026–2027 · Hacettepe University
MAT123 | Mathematics I (Calculus I)
🔒 Protected materials
f′(x) = lim [f(x+h) − f(x)] / h
Limits · Derivatives · Integrals
General InformationMaterialsAssignmentsAnnouncementsExams
Course typeCompulsory
Prerequisite(s)None
Co-requisite(s)None
ModeFace-to-face
Teaching methodsLecture, discussion, question–answer
Course Objective
To introduce the fundamental topics of analysis and teach the concepts of limits, derivatives, integrals and their applications.
Learning Outcomes
Elementary functions; limits and continuity; derivatives and graphing; maximum and minimum problems; integration methods and improper integrals; applications of integration; sequences and series; convergence tests; Taylor and Maclaurin series.
Course Content
Functions, limits and continuity; derivatives and applications; graph sketching; maxima and minima; definite and indefinite integrals; integration techniques; improper integrals; areas, volumes, surface area and arc length; sequences and series; convergence tests; Taylor and Maclaurin series.
References
Thomas, Calculus and Analytic Geometry, Addison-Wesley, 1996 · Silverman, Calculus with Analytic Geometry, Prentice-Hall, 1985 · Adams, Calculus: A Complete Course, Addison-Wesley, 2003 · Balcı, Temel ve Genel Matematik I & II, 2000.
The downloadable files in this preview package are not yet access-controlled. Course passwords will be enforced at the hosting/server level; passwords are intentionally not stored in the HTML source.
← Back to Teaching2026–2027 · Hacettepe University
MAT124 | Mathematics II (Calculus II)
🔒 Protected materials
∇f · dr ∬_D f(x,y) dA
Vectors · Multivariable Calculus
General InformationMaterialsAssignmentsAnnouncementsExams
Course typeCompulsory
Prerequisite(s)MAT123
Co-requisite(s)None
ModeFace-to-face
Teaching methodsLecture, discussion, question–answer
Course Objective
To introduce fundamental topics of analysis and teach the concepts of limits, derivatives and integrals for scalar- and vector-valued functions together with their applications.
Learning Outcomes
Recognize and sketch conic sections; work with vectors and vector-valued functions; interpret limits, derivatives and integrals of vector-valued functions; compute partial derivatives and multiple integrals; define vector fields and apply their integral concepts.
Course Content
Conic sections and polar coordinates; vectors and geometry of space; vector-valued functions; partial derivatives; multiple integrals; vector fields and their integrals.
References
Thomas, Calculus and Analytic Geometry, Addison-Wesley, 1996 · Silverman, Calculus with Analytic Geometry, Prentice-Hall, 1985 · Adams, Calculus: A Complete Course, Addison-Wesley, 2003 · Balcı, Temel ve Genel Matematik I & II, 2000.
The downloadable files in this preview package are not yet access-controlled. Course passwords will be enforced at the hosting/server level; passwords are intentionally not stored in the HTML source.
← Back to Teaching2026–2027 · Türkiye–Azerbaijan University
Differential Equations
🔒 Protected materials
y′ + p(x)y = q(x)
ODEs · Laplace · PDEs
General InformationMaterialsAssignmentsAnnouncementsExams
Differential Equations · 2026–2027
Course Objectives
The objectives of this course are to introduce students to the concept of a differential equation, basic techniques for solving certain classes of differential equations, especially linear equations, and connections between qualitative features of equations and their solutions. Connections to problems from the physical world are emphasized. In addition to ordinary differential equations, the course introduces selected partial differential equations.
Course Content
First-order equations and applications; higher-order linear differential equations; power-series solutions; Laplace transform and initial-value problems; systems of linear differential equations; introduction to partial differential equations.
Course Learning Outcomes
- Classify and identify different types of differential equations.
- Solve important classes of ordinary differential equations and interpret their qualitative behaviour.
- Apply linear algebra to solve linear ODEs and systems.
- Model physical phenomena using differential equations and interpret solutions physically.
- Use power-series methods for second-order linear differential equations.
- Apply the Laplace transform to differential equations.
- Use separation of variables and Fourier series for basic partial differential equations.
The downloadable files in this preview package are not yet access-controlled. Course passwords will be enforced at the hosting/server level; passwords are intentionally not stored in the HTML source.
Weekly Teaching Schedule Fall 2026
Hacettepe University · Türkiye–Azerbaijan University
Monday
Türkiye–Azerbaijan UniversityDifferential Equations09:40–12:30 · English
Tuesday
Türkiye–Azerbaijan UniversityDifferential Equations09:40–12:30 · English
Wednesday
Hacettepe UniversityMAT123 · Mathematics IElectrical & Electronics Engineering · 09:40–11:30 · English
MAT124 · Mathematics IIEnvironmental Engineering · 11:40–13:30 · English
Thursday
Hacettepe UniversityMAT124 · Mathematics IIEnvironmental Engineering · 10:40–12:30 · English
MAT123 · Mathematics IElectrical & Electronics Engineering · 13:40–15:30 · English
Friday
Hacettepe UniversityMAT124 · Mathematics IIEnvironmental Engineering · 10:40–12:30 · English
MAT123 · Mathematics IElectrical & Electronics Engineering · 13:40–15:30 · English